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https://www.readbyqxmd.com/read/28441386/graft-derived-cell-free-dna-a-noninvasive-early-rejection-and-graft-damage-marker-in-liver-transplantation-a-prospective-observational-multicenter-cohort-study
#1
Ekkehard Schütz, Anna Fischer, Julia Beck, Markus Harden, Martina Koch, Tilo Wuensch, Martin Stockmann, Björn Nashan, Otto Kollmar, Johannes Matthaei, Philipp Kanzow, Philip D Walson, Jürgen Brockmöller, Michael Oellerich
BACKGROUND: Graft-derived cell-free DNA (GcfDNA), which is released into the blood stream by necrotic and apoptotic cells, is a promising noninvasive organ integrity biomarker. In liver transplantation (LTx), neither conventional liver function tests (LTFs) nor immunosuppressive drug monitoring are very effective for rejection monitoring. We therefore hypothesized that the quantitative measurement of donor-derived cell-free DNA (cfDNA) would have independent value for the assessment of graft integrity, including damage from acute rejection...
April 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28429561/cfdna-screening-performance-accounting-for-and-reducing-test-failures
#2
EDITORIAL
H Cuckle
Over several decades antenatal screening for Down's syndrome steadily evolved from the initial concept of a single second trimester maternal serum marker to complex protocols involving the combination of multiple serum and fetal ultrasound markers, determined within-trimester or sequentially across-trimesters.
April 21, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28429088/an-snp-panel-for-the-analysis-of-paternally-inherited-alleles-in-maternal-plasma-using-ion-torrent-pgm
#3
Donggui Yang, Hao Liang, Shaobin Lin, Qing Li, Xiaoyan Ma, Jun Gao, Hongyu Sun, Qingqing Chen, Jianzhu Wu, Xueling Ou
Researchers have sought to develop an effective protocol for paternity analysis using cell-free DNA (cfDNA) in maternal plasma. The use of massively parallel sequencing (MPS) technology for SNP testing is attractive because of its high-throughput capacity and resolution to single-base precision. In this study, we designed a customized SNP panel for cfDNA sequencing that includes 720 short amplicons (< 140 bp) targeting SNPs on the autosome and Y chromosome. The systemic performance was evaluated using the Ion Torrent PGM, indicating balanced coverage among most of the included loci, except for 78 poorly performing SNPs that were observed to have an inconsistent allele balance, lower coverage reads or high background signals...
April 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28424857/extraction-of-cell-free-dna-from-urine-using-polylysine-coated-silica-particles
#4
Sho Takano, Qingjiang Hu, Takaki Amamoto, Paulo Refinetti, Koshi Mimori, Takashi Funatsu, Masaru Kato
DNA analysis is used for a variety of purposes, including disease diagnosis and DNA profiling; this involves extracting DNA from living organisms. In this study, we prepared polycationic silica particles to extract DNA that has the negatively charged phosphate backbone from solution. The coated particles were prepared by mixing conventional silica gel particles and poly-Lys; these particles could efficiently extract 1.3 μg of cell-free DNA from 50 mL of (male) urine. It is expected that these easily prepared particles (just a mixture of two commercially available chemicals) can be used as a noninvasive diagnostic tool for genetic disorders such as cancer, diabetes, and hypertension...
April 19, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28423190/the-clinical-utility-of-genome-wide-non-invasive-prenatal-screening
#5
Francesco Fiorentino, Sara Bono, Francesca Pizzuti, Sara Duca, Arianna Polverari, Monica Faieta, Marina Baldi, Laura Diano, Francesca Spinella
OBJECTIVE: In this study, we expanded conventional cell-free fetal DNA(cfDNA)-based non-invasive prenatal testing(NIPT) to cover the entire genome. We aimed to compare the performance of the two test in a large general population of pregnant women, in order to assess the clinical utility of the genome-wide screening. METHOD: Genome-wide cfDNA analysis was offered to 12.114 pregnant women undergoing NIPT for common fetal aneuploidy. Sequencing data were analyzed using an algorithm optimized to identify aneuploidies and subchromosomal aberrations...
April 17, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28416944/evaluation-of-digital-pcr-as-a-technique-for-monitoring-acute-rejection-in-kidney-transplantation
#6
Hyeseon Lee, Young-Mi Park, Yu-Mee We, Duck Jong Han, Jung-Woo Seo, Haena Moon, Yu-Ho Lee, Yang-Gyun Kim, Ju-Young Moon, Sang-Ho Lee, Jong-Keuk Lee
Early detection and proper management of kidney rejection are crucial for the long-term health of a transplant recipient. Recipients are normally monitored by serum creatinine measurement and sometimes with graft biopsies. Donor-derived cell-free deoxyribonucleic acid (cfDNA) in the recipient's plasma and/or urine may be a better indicator of acute rejection. We evaluated digital PCR (dPCR) as a system for monitoring graft status using single nucleotide polymorphism (SNP)-based detection of donor DNA in plasma or urine...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28414925/reversion-of-brca1-2-germline-mutations-detected-in-circulating-tumor-dna-from-patients-with-high-grade-serous-ovarian-cancer
#7
Elizabeth L Christie, Sian Fereday, Ken Doig, Swetansu Pattnaik, Sarah-Jane Dawson, David D L Bowtell
Purpose Germline BRCA1 or BRCA2 mutations in patients with high-grade serous ovarian cancer (HGSC) are associated with favorable responses to chemotherapy. However, secondary intragenic (reversion) mutations that restore protein function lead to clinically significant rates of acquired resistance. The goal of this study was to determine whether reversion mutations could be found in an unbiased manner in circulating cell-free DNA (cfDNA) to predict treatment response in HGSC. Patients and Methods Plasma and tumor samples were obtained from 30 patients with HGSC with either BRCA1 or BRCA2 germline mutation...
April 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28412848/proteomic-profile-of-serum-of-pregnant-women-carring-a-fetus-with-down-syndrome-using-nano-uplc-q-tof-ms-ms-technology
#8
Graciela Arelí López-Uriarte, Carlos Horacio Burciaga Flores, Víctor Manuel Torres de la Cruz, María Magdalena Medina Aguado, Viviana Maricela Gómez Puente, Liliana Nayeli Romero Gutiérrez, Laura Elia Martínez de Villarreal
INTRODUCTION: Prenatal diagnosis of Down syndrome (DS) is based on the calculated risk of maternal age, biochemical and ultrasonographic markers and recently by cfDNA. Differences in proteomic profiles may give an opportunity to find new biomarkers. OBJECTIVE: Characterize proteome of serum of mothers carrying DS fetus. MATERIAL AND METHODS: Blood serum samples of three groups of women were obtained, a) 10 non-pregnant, b) 10 pregnant with healthy fetus by ultrasound evaluation, c) 9 pregnant with DS fetus; Sample preparation was as follow: Albumin/IgG depletion, desalting, and trypsin digestion; the process was performed in nanoUPLC MS/MS...
April 16, 2017: Journal of Maternal-fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/28405680/optimal-method-for-quantitative-detection-of-plasma-egfr-t790m-mutation-using-droplet-digital-pcr-system
#9
Ken Suzawa, Hiromasa Yamamoto, Kadoaki Ohashi, Shinsuke Hashida, Shuta Tomida, Toshio Kubo, Yuho Maki, Junichi Soh, Kazunori Tsukuda, Katsuyuki Kiura, Shinichiro Miyoshi, Shinichi Toyooka
Though patients with EGFR mutations are initially responsive to EGFR-tyrosine kinase inhibitors (TKIs), most tumors ultimately acquire resistance to EGFR-TKIs. The most frequently reported mechanism is EGFR T790M mutation. In this study, using a droplet digital PCR (ddPCR) system, we assessed optimal conditions for a mutation detection assay for EGFR T790M obtained from circulating cell-free DNA (cfDNA) in plasma. The advantages of locked nucleic acids (LNA) probe, short amplicon size, and blocking oligo using peptide nucleic acids (PNA) were assessed using control DNAs from cell lines to improve the sensitivity of mutation detection...
May 2017: Oncology Reports
https://www.readbyqxmd.com/read/28400427/circulating-dna-demonstrates-convergent-evolution-and-common-resistance-mechanisms-during-treatment-of-colorectal-cancer
#10
Alain R Thierry, Brice Pastor, Zhi-Qin Jiang, Anastasia Katsiampoura, Christine Parseghian, Jonathan M Loree, Michael J Overman, Cynthia Sanchez, Safia El Messaoudi, Marc Ychou, Scott Kopetz
Purpose: Liquid biopsies allow the tracking of clonal dynamics and detection of mutations during treatment. <p>Experimental design: We evaluated under blinded conditions the ability of cell free DNA (cfDNA) to detect RAS/BRAF mutations in the plasma of 42 metastatic colorectal cancer patients treated on a phase Ib/II trial of FOLFOX and dasatinib, with or without cetuximab. Results: Prior to treatment, sequencing of archival tissue detected mutations in 25/42 patients (60%), while the cfDNA assay detected mutations in 37/42 patients (88%)...
April 11, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28397325/analysis-of-cell-free-dna-in-maternal-blood-in-screening-for-aneuploidies-updated-meta-analysis
#11
REVIEW
M M Gil, V Accurti, B Santacruz, M N Plana, K H Nicolaides
OBJECTIVE: To review clinical validation or implementation studies of maternal blood cell-free (cf) DNA analysis and define the performance of screening for fetal trisomies 21, 18 and 13 and sex chromosome aneuploidies. DATA SOURCES: Searches of PubMed, Embase and the Cochrane library were performed to identify all peer-reviewed articles on cfDNA testing in screening for aneuploidies between January 2011, when the first such study was published and 31 December 2016...
April 11, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28393575/using-circulating-cell-free-dna-to-monitor-personalized-cancer-therapy
#12
Michael Oellerich, Ekkehard Schütz, Julia Beck, Philipp Kanzow, Piers N Plowman, Glen J Weiss, Philip D Walson
High-quality genomic analysis is critical for personalized pharmacotherapy in patients with cancer. Tumor-specific genomic alterations can be identified in cell-free DNA (cfDNA) from patient blood samples and can complement biopsies for real-time molecular monitoring of treatment, detection of recurrence, and tracking resistance. cfDNA can be especially useful when tumor tissue is unavailable or insufficient for testing. For blood-based genomic profiling, next-generation sequencing (NGS) and droplet digital PCR (ddPCR) have been successfully applied...
April 10, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/28388340/offering-prenatal-screening-in-the-age-of-genomic-medicine-a-practical-guide
#13
Megan Allyse, Umut Aypar, Natasha Bonhomme, Sandra Darilek, Michael Dougherty, Ruth Farrell, Wayne Grody, W Edward Highsmith, Marsha Michie, Mark Nunes, Laura Otto, Rebecca Pabst, Glenn Palomaki, Cassandra Runke, Richard R Sharp, Brian Skotko, Katie Stoll, Myra Wick
AIMS: In September, 2015, Mayo Clinic convened a panel of national thought leaders on prenatal screening, medical genetics, and obstetrics and gynecology practice. RESULTS: During the 2-day symposium, participants discussed the implications of the shift toward broader prenatal screening using cell-free placental DNA in maternal serum (cfDNA screening). Key topics included challenges around the pace of change in the prenatal screening market, uncertainty around reimbursement, meeting the need for patient counseling, and potential challenges in interpreting and returning cfDNA screening results...
April 7, 2017: Journal of Women's Health
https://www.readbyqxmd.com/read/28383679/ezmap-a-simple-pipeline-for-reproducible-analysis-of-the-human-virome
#14
Patrick Czeczko, Steven C Greenway, A P Jason de Koning
Summary: In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully-automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome...
April 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28382702/post-surgery-circulating-free-tumor-dna-is-a-predictive-biomarker-for-relapse-of-lung-cancer
#15
Wenwei Hu, Yang Yang, Longzhen Zhang, Jianxin Yin, Jingwei Huang, Lei Huang, Hua Gu, Gening Jiang, Jianmin Fang
Cancer cells release DNA fragments into plasma as circulating free DNA (cfDNA). However, quantitative measurement of tumor-derived DNA in cfDNA remains challenge. The purpose of this study was to quantitatively assess tumor-derived DNA in lung cancer patients. By optimizing competitive allele-specific TaqMan PCR (CAST-PCR), we assessed the copy number of mutated Kirsten rat sarcoma viral oncogene homolog (KRAS) and epidermal growth factor receptor (EGFR) alleles in the pre/post surgery plasma of 168 lung cancer patients...
April 5, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28378885/global-hypomethylation-is-an-independent-prognostic-factor-in-diffuse-large-b-cell-lymphoma
#16
Jakob Werner Hansen, Christian Garde, Fazila Asmar, Dorte Tholstrup, Søren Sommer Kristensen, Helga D Munch-Petersen, Elisabeth Ralfkiaer, Peter Brown, Kirsten Grønbaek, Lasse Sommer Kristensen, Eileen Wedge
Global hypomethylation has been linked to disease progression in several cancers, but has not been reported for Diffuse Large B Cell Lymphoma (DLBCL). This study aimed to assess global methylation in DLBCL and describe its prognostic value. Mean LINE1 methylation, a validated surrogate measure for global methylation, was measured in DNA from 67 tumor biopsies. Additionally, cell-free circulating DNA (cfDNA) in plasma samples from 74 patients was tested to assess the feasibility of global hypomethylation as a biomarker in liquid biopsies...
April 5, 2017: American Journal of Hematology
https://www.readbyqxmd.com/read/28374559/incorporating-thyroid-markers-in-down-syndrome-screening-protocols
#17
Ishraq Dhaifalah, Tomas Salek, Dagmar Langova, Howard Cuckle
OBJECTIVE: The article aimed to assess the benefit of incorporating maternal serum thyroid disease marker levels (thyroid-stimulating hormone and free thyroxine) into first trimester Down syndrome screening protocols. METHODS: Statistical modelling was used to predict performance with and without the thyroid markers. Two protocols were considered: the combined test and the contingent cell-free DNA (cfDNA) test, where 15-40% women are selected for cfDNA because of increased risk based on combined test results...
April 3, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28366031/what-do-the-new-american-college-of-medical-genetics-and-genomics-acmg-guidelines-mean-for-the-provision-of-non-invasive-prenatal-genetic-screening
#18
Megan Allyse, Myra J Wick
In 2016, the American College of Medical Genetics and Genomics updated their practice guidelines on the provision of non-invasive prenatal genomic screening using cell-free DNA. This article lays out the changes to the guidelines and their implications for clinical practice. Impact Statement What is already known on this subject.cfDNA is being translated into prenatal clinical practice at a rapid pace. Various professional societies have attempted to provide ongoing guidance for this translation. What the results of this study add...
April 1, 2017: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28365952/cell-free-dna-as-biomarker-and-source-for-mutation-detection-in-primary-colorectal-cancer
#19
Aleksandra Nikolic, Marina Vlajnic, Momcilo Ristanovic, Jelena Petrovic, Ivan Dimitrijevic, Zoran Krivokapic, Dragica Radojkovic
PURPOSE: To analyze if cell-free (cf)DNA levels and the presence of KRAS and BRAF mutations in serum could be used as diagnostic biomarkers in patients with primary colorectal cancer (CRC). METHODS: This study included 92 individuals who were operated due to primary CRC (N=52;study group) and to hemorrhoids (N=40;control group). Serum cfDNA levels were measured with real-time PCR (RT-PCR) using PicoGreen dsDNA quantitation reagent. Colorectal tissue and related blood and serum samples taken at the time of surgery were subjected to DNA extraction and analysis of KRAS and BRAF mutations based on multiplex SNaPshot assay and DNA sequencing...
January 2017: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/28362710/detection-of-loss-of-heterozygosity-loh-using-circulating-cell-free-dna-cfdna-by-fluorescence-based-multiplex-pcr-for-identification-of-patients-with-prostate-cancer
#20
S-Maryam Seyedolmohadessin, Mohammad T Akbari, Zahra Nourmohammadi, Abbas Basiri, Gholamreza Pourmand
Several lines of evidence suggest that loss of heterozygosity (LOH) in specific chromosomal regions is a common mechanism for the inactivation of tumor-suppressor genes that are implicated in the pathogenesis of prostate cancer (PCa). Short tandem repeat (STR) sequences are extremely reliable genetic markers for the detection of LOH associated with cancers. Hence, in the current study, we investigated the detection of LOH at 6 STR markers (D8S360, D9S1748, D9S171, D8S137, D6S1631, and THRB) using blood circulating cell-free DNA (cfDNA), which can be used to distinguish PCa from benign prostatic hyperplasia (BPH)...
March 30, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
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